/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
Hashtable[] total;
boolean canonicaliseAa = true; // if true then conservation calculation will
- // map all symbols to canonical aa numbering
- // rather than consider conservation of that
- // symbol
+
+ // map all symbols to canonical aa numbering
+ // rather than consider conservation of that
+ // symbol
/** Stores calculated quality values */
public Vector quality;
this.end = end;
maxLength = end - start + 1; // default width includes bounds of
- // calculation
+ // calculation
int s, sSize = sequences.size();
SequenceI[] sarray = new SequenceI[sSize];
}
/**
- * Translate sequence i into a numerical
- * representation and store it in the i'th position of the seqNums array.
+ * Translate sequence i into a numerical representation and store it in the
+ * i'th position of the seqNums array.
*
* @param i
*/
}
sqnum = new int[len + 1]; // better to always make a new array -
- // sequence can change its length
+ // sequence can change its length
sqnum[0] = sq.hashCode();
for (j = 1; j <= len; j++)
}
/*****************************************************************************
- * count conservation for the j'th column of the alignment
+ * count conservation for the j'th column of the alignment
+ *
* @return { gap count, conserved residue count}
*/
public int[] countConsNGaps(int j)
* maxj = -1;
*
* for (int j=0;j<24;j++) { if (cons2[i][j] > max) { max = cons2[i][j];
- * maxi = i; maxj = j; }
- * } }
+ * maxi = i; maxj = j; } } }
*/
}
}